that's because 99% of the time someone uses "unrealistic" in these forums it's really a disconnect between reality and perception.
i'll trust that the game developer's research is better than my 'eye' if i have a feeling of frustration due to injuries. a string of inuries hits your team and all of a sudden it's "elevated."
spot on for batters -- contact @ 150-160+ with any other complimentary skills and they are HoF with health. pitching is a bit more complicated, but similar. you get a SP with ~max scale stuff they are wicked (only takes a few 150-175 pitches and average velo/move+/control+).
the age stuff: if oyu have minimum age requirment, make sure the ages of created players jive with that value. ie you likely don't want to leave it at 0/0 min/max age if you want 40year old rookies. maybe i am wrong, but either way do a little trial and error with relative settings and you should be able to iron this out. (i am making assumptions*)
phantom teams? something odd happened if that's true or they weren't removed correctly. double check League Settings -> League Structure. make sure to select the mil with the phantom team in the drop-down in top-right. also, on any page, look for "available actions" - some option/functions are only in this drop-down or just simply easier from here.
difference between independent and major and international etc: mostly just semantics, but the defaults of each are slightly different. for example, an independent league starts with a very low default reputation, and it's PCM's are different. all of the differences can be edited to be equal to each other, if you wanted to do so.
if you want an independent league with ML talent, make sure it's rep is high, it's salary settings are high enough to compete with any other leagues in world, change PCM's to "1.000", amend LT/LTM (leauge totals/league totals modifers) ... etc etc.. you get the point..
basically it's just setting a skeleton for the league so that you don't have to do all that work... maybe just amend them a small amount to get what you want, insteadof re-doing the entire thing for each type of league.
regional stuff: not sure if you can use a State as a region. someone else either this release or last made a league similar to what you are expressing interest. i'd search forums, i cannot recall specifics, but he did get it to work if i recall.
you can make a world and structure it as you need, at the least. or edit an existing one -- XML editor will be useful.. notepad++ is a free one that's good. color-codes stuff, makes it easier to read/edit etc.
so if it can only be a "country" then you make Maryland a "country" in game terms only. asthetic only. never delved into the xml labels, but likely don't have to set it as a "Country" maybe not.
i want to say the old thread was a league in Australia.. so do a "ootp" + "<regions of australia>" like queensland (spelling) ... heh they call them states there.. 6 in one, half dozen the other. a rose is a rose is a rose blah blah.
in this game retired essentially equals dead... the game will never unretire a 150year old in my experience. so, if you don't want zombies, refrain from doing so
easy fix there, since it's self-inflicted.
just a guess:
but seriously, i wouldn't care either way if tehy "died", since it's not real. i think some people get a lil emotional about that topic though. they anthropomorphize an inanimate object like software. i think ootp avoids the situation on purpose. i wouldn't blame them. someone freaked out in forums that they didn't remove someone that died recently... not a big name like the floriday pitcher. a bit unreasonable to expect them to check obits for 10,000's of people constantly. a little lag should be forgiven for something as unimportant as a video game.